The former youth coach at Crewe Alexandra denied seven counts of indecent assault on a boy and one count of attempted buggery.
All the offences are alleged to have happened between 1981 and 1986, when the victim was under 16.
Mr Bennell, aged 63, appearing via videolink from HMP Woodhill in Milton Keynes at Chester Crown Court, answered "not guilty" to all the charges as they were put to him.
The ex-coach, who also worked at Manchester City, Stoke City and junior teams in north-west England and the Midlands, was remanded in custody until March 20.
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Owen Edwards, prosecuting, told the court the alleged victim "preserves his anonymity".
Judge Roger Dutton reminded the press and members of the public in court that any identification of the alleged complainant "will be treated very seriously" by the courts.